Abstract
Pneumonia is the sixth largest cause of death in the UK. It is usually caused by Streptococcus pneumoniae, which healthy individuals can carry in their nose without symptoms of disease. Antimicrobial resistance further increases mortality and morbidity associated with pneumococcal infection, although few studies have analysed resistance in naturally circulating pneumococcal isolates in adult populations. Here, we report on the resistome and associated mobile genetic elements within circulating pneumococcus isolated from adult volunteers enrolled in the experimental human pneumococcal colonisation (EHPC) research program at the Liverpool School of Tropical Medicine, UK. Pneumococcal isolates collected from 30 healthy asymptomatic adults who had volunteered to take part in clinical research were screened for antibiotic susceptibility to erythromycin and tetracycline, and whole-genome sequenced. The genetic context of resistance to one or both antibiotics in four isolates was characterised bioinformatically, and any association of the resistance genes with mobile genetic elements was determined. Tetracycline and macrolide resistance genes [tet(M), erm(B), mef(A), msr(D)] were detected on known Tn916-like integrative and conjugative elements, namely Tn6002 and Tn2010, and tet(32) was found for the first time in S. pneumoniae located on a novel 50 kb genomic island. The widespread use of pneumococcal conjugate vaccines impacts on serotype prevalence and transmission within the community. It is therefore important to continue to monitor antimicrobial resistance (AMR) genes present in both vaccine types and non-vaccine types in response to contemporary antimicrobial therapies and characterise the genetic context of acquired resistance genes to continually optimise antibiotic therapies.
Highlights
Pneumonia is the largest cause of vaccine-preventable death in children under five [1] and a major problem in adults causing high levels of hospitalisations of at risks groups such as the elderly, Genes 2020, 11, 625; doi:10.3390/genes11060625 www.mdpi.com/journal/genesGenes 2020, 11, 625 people with chronic lung disease and asthmatics [2]
Serotype prevalence varies in different age groups and geographic regions in each population exposed to antibiotics and pneumococcal vaccination [12]
The remaining 26 isolates did not grow at double breakpoint concentrations of antibiotics which agrees with the susceptibility previously reported [16]
Summary
Pneumonia is the largest cause of vaccine-preventable death in children under five [1] and a major problem in adults causing high levels of hospitalisations of at risks groups such as the elderly, Genes 2020, 11, 625; doi:10.3390/genes11060625 www.mdpi.com/journal/genes. The bacterium Streptococcus pneumoniae, known as pneumococcus and the major cause of pneumonia, naturally inhabits the nasopharynx of 40–95% of infants and 10–25% of adults without causing disease [3,4,5]. PCV vaccination has reduced carriage of vaccine-types (VT), carriage of non-vaccine types (NVT) has increased (serotype replacement). This indicates that the competition of different pneumococcal serotypes within the respiratory niche is a prerequisite for bacterial colonisation [11]. S. pneumoniae isolates from naturally colonised volunteers enrolled in the EHPC clinical studies from baseline samples [16]. We analysed 30 of these isolates from this unique pool of pneumococci collected at baseline between 2010 and 2017 in Liverpool, UK, to ascertain any relationship between circulating AMR genes and mobile genetic elements
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